AutoCloner

Multiple sequence alignment - TraesCS5D01G257300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)

BLAST Results

Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

	qseqid	sseqid	percentage.identical	alignment.length	no.mismatch	no.gap.openings	qstart	qend	sstart	send	evalue	bitscore
0	TraesCS5D01G257300	chr5D	100.000	2492	0	0	1	2492	363887346	363889837	0.000000e+00	4602.0
1	TraesCS5D01G257300	chr5D	94.705	1511	60	11	987	2492	114516785	114518280	0.000000e+00	2329.0
2	TraesCS5D01G257300	chr5D	95.000	380	15	1	619	994	84221155	84220776	5.930000e-166	593.0
3	TraesCS5D01G257300	chr5D	87.760	384	37	5	229	612	363172923	363173296	8.180000e-120	440.0
4	TraesCS5D01G257300	chr3D	95.433	1511	58	8	987	2492	546486444	546487948	0.000000e+00	2398.0
5	TraesCS5D01G257300	chr3D	95.526	380	13	1	619	994	527509677	527510056	2.740000e-169	604.0
6	TraesCS5D01G257300	chr3D	94.615	390	17	3	609	994	546485984	546486373	3.550000e-168	601.0
7	TraesCS5D01G257300	chr7D	95.238	1512	59	9	987	2492	90563157	90561653	0.000000e+00	2381.0
8	TraesCS5D01G257300	chr7D	95.093	1508	59	9	987	2492	22901065	22899571	0.000000e+00	2361.0
9	TraesCS5D01G257300	chr7D	94.911	1513	60	12	990	2492	605600303	605601808	0.000000e+00	2351.0
10	TraesCS5D01G257300	chr7D	94.301	386	20	1	611	994	246983058	246982673	7.680000e-165	590.0
11	TraesCS5D01G257300	chr1D	95.178	1514	60	9	987	2492	25464765	25466273	0.000000e+00	2379.0
12	TraesCS5D01G257300	chr2B	94.914	1514	64	11	987	2492	173502951	173501443	0.000000e+00	2357.0
13	TraesCS5D01G257300	chr7B	94.643	1512	71	7	987	2492	702337734	702339241	0.000000e+00	2335.0
14	TraesCS5D01G257300	chr7B	94.974	378	14	3	615	991	1776635	1776262	2.760000e-164	588.0
15	TraesCS5D01G257300	chr7B	95.187	374	13	2	619	991	692881452	692881821	9.930000e-164	586.0
16	TraesCS5D01G257300	chr7B	76.000	325	66	10	299	617	578706070	578706388	9.230000e-35	158.0
17	TraesCS5D01G257300	chr1B	94.643	1512	67	9	987	2492	332064520	332063017	0.000000e+00	2331.0
18	TraesCS5D01G257300	chr6A	94.103	390	16	4	605	991	617222885	617222500	9.930000e-164	586.0
19	TraesCS5D01G257300	chr6B	94.723	379	15	2	614	991	660437748	660437374	3.570000e-163	584.0
20	TraesCS5D01G257300	chr3A	94.010	384	18	2	609	991	9952648	9953027	5.980000e-161	577.0
21	TraesCS5D01G257300	chr5B	93.169	366	21	4	1	366	429645661	429646022	3.650000e-148	534.0
22	TraesCS5D01G257300	chr5B	91.892	222	18	0	397	618	429646020	429646241	6.690000e-81	311.0
23	TraesCS5D01G257300	chr4A	82.022	89	15	1	480	567	37791503	37791591	9.560000e-10	75.0
24	TraesCS5D01G257300	chr4B	80.899	89	16	1	480	567	526744168	526744256	4.450000e-08	69.4
25	TraesCS5D01G257300	chr2A	94.444	36	2	0	532	567	12147036	12147001	3.460000e-04	56.5

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS5D01G257300	chr5D	363887346	363889837	2491	False	4602.0	4602	100.0000	1	2492	1	chr5D.!!$F3	2491
1	TraesCS5D01G257300	chr5D	114516785	114518280	1495	False	2329.0	2329	94.7050	987	2492	1	chr5D.!!$F1	1505
2	TraesCS5D01G257300	chr3D	546485984	546487948	1964	False	1499.5	2398	95.0240	609	2492	2	chr3D.!!$F2	1883
3	TraesCS5D01G257300	chr7D	90561653	90563157	1504	True	2381.0	2381	95.2380	987	2492	1	chr7D.!!$R2	1505
4	TraesCS5D01G257300	chr7D	22899571	22901065	1494	True	2361.0	2361	95.0930	987	2492	1	chr7D.!!$R1	1505
5	TraesCS5D01G257300	chr7D	605600303	605601808	1505	False	2351.0	2351	94.9110	990	2492	1	chr7D.!!$F1	1502
6	TraesCS5D01G257300	chr1D	25464765	25466273	1508	False	2379.0	2379	95.1780	987	2492	1	chr1D.!!$F1	1505
7	TraesCS5D01G257300	chr2B	173501443	173502951	1508	True	2357.0	2357	94.9140	987	2492	1	chr2B.!!$R1	1505
8	TraesCS5D01G257300	chr7B	702337734	702339241	1507	False	2335.0	2335	94.6430	987	2492	1	chr7B.!!$F3	1505
9	TraesCS5D01G257300	chr1B	332063017	332064520	1503	True	2331.0	2331	94.6430	987	2492	1	chr1B.!!$R1	1505
10	TraesCS5D01G257300	chr5B	429645661	429646241	580	False	422.5	534	92.5305	1	618	2	chr5B.!!$F1	617

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
770	771	0.39382	ACGTTTTGACTCGGCCCTTA	59.606	50.0	0.0	0.0	0.0	2.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1702	1793	0.323725	ACGCTCTGAATTTGGCCCAT	60.324	50.0	0.0	0.0	0.0	4.0	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
38	39	4.264460	AGGCGCCAACAATCAAATTTAA	57.736	36.364	31.54	0.00	0.00	1.52
156	157	7.418025	GGTGTACTTCTTAAGCACCAGATCTAT	60.418	40.741	18.82	0.00	46.29	1.98
270	271	2.281091	CCAAGGGCATGCAGGGAT	59.719	61.111	21.36	0.00	0.00	3.85
328	329	9.097257	CTTTAAGATTTGTCAACATGTTTGGTT	57.903	29.630	8.77	0.00	0.00	3.67
362	363	5.810080	AATACTGTAGGCTAGGGTCATTC	57.190	43.478	0.00	0.00	0.00	2.67
363	364	3.116096	ACTGTAGGCTAGGGTCATTCA	57.884	47.619	0.00	0.00	0.00	2.57
364	365	3.658725	ACTGTAGGCTAGGGTCATTCAT	58.341	45.455	0.00	0.00	0.00	2.57
365	366	3.389329	ACTGTAGGCTAGGGTCATTCATG	59.611	47.826	0.00	0.00	0.00	3.07
366	367	2.104792	TGTAGGCTAGGGTCATTCATGC	59.895	50.000	0.00	0.00	0.00	4.06
367	368	1.216064	AGGCTAGGGTCATTCATGCA	58.784	50.000	0.00	0.00	0.00	3.96
368	369	1.779092	AGGCTAGGGTCATTCATGCAT	59.221	47.619	0.00	0.00	0.00	3.96
369	370	1.884579	GGCTAGGGTCATTCATGCATG	59.115	52.381	21.07	21.07	0.00	4.06
370	371	1.268899	GCTAGGGTCATTCATGCATGC	59.731	52.381	22.25	11.82	0.00	4.06
371	372	2.860009	CTAGGGTCATTCATGCATGCT	58.140	47.619	22.25	13.14	0.00	3.79
372	373	2.154567	AGGGTCATTCATGCATGCTT	57.845	45.000	22.25	10.16	0.00	3.91
373	374	2.463752	AGGGTCATTCATGCATGCTTT	58.536	42.857	22.25	5.94	0.00	3.51
374	375	2.835764	AGGGTCATTCATGCATGCTTTT	59.164	40.909	22.25	3.38	0.00	2.27
375	376	2.933906	GGGTCATTCATGCATGCTTTTG	59.066	45.455	22.25	14.94	0.00	2.44
376	377	2.933906	GGTCATTCATGCATGCTTTTGG	59.066	45.455	22.25	7.87	0.00	3.28
377	378	2.350498	GTCATTCATGCATGCTTTTGGC	59.650	45.455	22.25	13.15	42.22	4.52
395	396	2.338140	GCAACTTTTGGCAGAGCTAC	57.662	50.000	0.00	0.00	0.00	3.58
409	410	2.169352	AGAGCTACATGTGTCATCCACC	59.831	50.000	9.11	0.00	43.85	4.61
474	475	7.619571	GCCTACTATATCGTTTGAATCGAAAGC	60.620	40.741	2.25	0.00	40.61	3.51
475	476	7.381408	CCTACTATATCGTTTGAATCGAAAGCA	59.619	37.037	2.25	0.00	40.61	3.91
508	509	7.090953	AGTTTCGTTTTCCTATTTGTGTTCA	57.909	32.000	0.00	0.00	0.00	3.18
658	659	1.956170	CAGTGGTGTCCGTGTGCTC	60.956	63.158	0.00	0.00	0.00	4.26
660	661	1.522806	GTGGTGTCCGTGTGCTCAA	60.523	57.895	0.00	0.00	0.00	3.02
687	688	1.741706	CCTCAGATGCGAATTGTGCTT	59.258	47.619	0.00	0.00	0.00	3.91
740	741	1.444553	CCGTGAACTCTGCCGTCTC	60.445	63.158	0.00	0.00	0.00	3.36
743	744	1.602605	TGAACTCTGCCGTCTCCGA	60.603	57.895	0.00	0.00	35.63	4.55
770	771	0.393820	ACGTTTTGACTCGGCCCTTA	59.606	50.000	0.00	0.00	0.00	2.69
814	815	4.120589	GACGACCAATTCTATTCAGACCC	58.879	47.826	0.00	0.00	0.00	4.46
929	931	2.505777	CAGCGACAGAGAGCACGG	60.506	66.667	0.00	0.00	35.48	4.94
959	963	2.407210	CGAGAGAGAGAGCACGGC	59.593	66.667	0.00	0.00	0.00	5.68
960	964	2.402572	CGAGAGAGAGAGCACGGCA	61.403	63.158	0.00	0.00	0.00	5.69
1218	1300	1.841302	TTTGGGTCGATGCTCTGGCT	61.841	55.000	0.00	0.00	39.59	4.75
1225	1307	1.406898	TCGATGCTCTGGCTAAGACTG	59.593	52.381	0.00	0.00	39.59	3.51
1283	1365	3.049674	CATGCTGCCACGAACGGT	61.050	61.111	0.00	0.00	0.00	4.83
1328	1410	1.115467	GAAGAGATGGAGGGCGAAGA	58.885	55.000	0.00	0.00	0.00	2.87
1389	1471	5.153950	TGAAGAAGAAGGTTAGGAAGCTC	57.846	43.478	0.00	0.00	38.49	4.09
1456	1538	5.008217	GCATTTGTAGGTATGGTAATCGCAA	59.992	40.000	0.00	0.00	0.00	4.85
1488	1570	6.610075	ATGTTGAAAATGTATGGAAAGGCT	57.390	33.333	0.00	0.00	0.00	4.58
1501	1583	5.191727	TGGAAAGGCTTGAATTATGGAGA	57.808	39.130	0.00	0.00	0.00	3.71
1572	1654	9.273016	TGTTGGTCAAAGTTGTTTAAATTTTGA	57.727	25.926	0.00	12.25	32.32	2.69
1747	1838	4.672587	CCAAGTGCAGGCTAGACTAATA	57.327	45.455	0.00	0.00	0.00	0.98
1991	2091	5.307204	ACCAAAATGTCATGGAAAATGTGG	58.693	37.500	0.00	0.00	39.12	4.17
1997	2097	2.821969	GTCATGGAAAATGTGGCTCAGT	59.178	45.455	0.00	0.00	0.00	3.41
2005	2105	3.788227	AATGTGGCTCAGTTCTGGTAA	57.212	42.857	0.00	0.00	0.00	2.85
2134	2235	2.203788	AGCTGGGGACTCGAACCA	60.204	61.111	9.91	4.55	0.00	3.67
2279	2380	5.102313	GTGAGAGTGGTTTTCCTTTGTTTG	58.898	41.667	0.00	0.00	41.38	2.93
2310	2411	2.008242	TTGGAGGGTTGGAATGTTGG	57.992	50.000	0.00	0.00	0.00	3.77
2352	2453	4.766891	CCACATGATTTTGGTTAGAGTGGT	59.233	41.667	0.00	0.00	39.21	4.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
38	39	8.574309	AGGGATTATCTCCTAGTCAAAGAAAT	57.426	34.615	1.28	0.00	44.28	2.17
51	52	8.437274	TTCTCATAAGGTAAGGGATTATCTCC	57.563	38.462	0.00	0.00	44.11	3.71
219	220	8.711457	CGTGCACATCATCTTGATATATAACAA	58.289	33.333	18.64	5.44	34.28	2.83
221	222	7.545615	TCCGTGCACATCATCTTGATATATAAC	59.454	37.037	18.64	0.00	34.28	1.89
270	271	1.227645	GCATGCATGCGTCCTCCTA	60.228	57.895	33.99	0.00	44.67	2.94
292	293	7.288810	TGACAAATCTTAAAGCAATTGGACT	57.711	32.000	7.72	0.00	0.00	3.85
293	294	7.437862	TGTTGACAAATCTTAAAGCAATTGGAC	59.562	33.333	7.72	0.00	0.00	4.02
297	298	8.891671	ACATGTTGACAAATCTTAAAGCAATT	57.108	26.923	0.00	0.00	0.00	2.32
328	329	9.555727	CTAGCCTACAGTATTAAAATGCCTTAA	57.444	33.333	0.00	0.00	0.00	1.85
369	370	1.331447	CTGCCAAAAGTTGCCAAAAGC	59.669	47.619	0.00	0.00	44.14	3.51
370	371	2.867975	CTCTGCCAAAAGTTGCCAAAAG	59.132	45.455	0.00	0.00	0.00	2.27
371	372	2.903798	CTCTGCCAAAAGTTGCCAAAA	58.096	42.857	0.00	0.00	0.00	2.44
372	373	1.473080	GCTCTGCCAAAAGTTGCCAAA	60.473	47.619	0.00	0.00	0.00	3.28
373	374	0.104671	GCTCTGCCAAAAGTTGCCAA	59.895	50.000	0.00	0.00	0.00	4.52
374	375	0.756442	AGCTCTGCCAAAAGTTGCCA	60.756	50.000	0.00	0.00	0.00	4.92
375	376	1.068264	GTAGCTCTGCCAAAAGTTGCC	60.068	52.381	0.00	0.00	0.00	4.52
376	377	1.608590	TGTAGCTCTGCCAAAAGTTGC	59.391	47.619	0.00	0.00	0.00	4.17
377	378	3.254166	ACATGTAGCTCTGCCAAAAGTTG	59.746	43.478	0.00	0.00	0.00	3.16
378	379	3.254166	CACATGTAGCTCTGCCAAAAGTT	59.746	43.478	0.00	0.00	0.00	2.66
379	380	2.816087	CACATGTAGCTCTGCCAAAAGT	59.184	45.455	0.00	0.00	0.00	2.66
380	381	2.816087	ACACATGTAGCTCTGCCAAAAG	59.184	45.455	0.00	0.00	0.00	2.27
381	382	2.813754	GACACATGTAGCTCTGCCAAAA	59.186	45.455	0.00	0.00	0.00	2.44
382	383	2.224499	TGACACATGTAGCTCTGCCAAA	60.224	45.455	0.00	0.00	0.00	3.28
383	384	1.347378	TGACACATGTAGCTCTGCCAA	59.653	47.619	0.00	0.00	0.00	4.52
384	385	0.975887	TGACACATGTAGCTCTGCCA	59.024	50.000	0.00	0.00	0.00	4.92
385	386	2.208431	GATGACACATGTAGCTCTGCC	58.792	52.381	0.00	0.00	0.00	4.85
386	387	2.208431	GGATGACACATGTAGCTCTGC	58.792	52.381	0.00	0.00	0.00	4.26
387	388	3.531934	TGGATGACACATGTAGCTCTG	57.468	47.619	0.00	0.00	0.00	3.35
409	410	6.889722	TGAAATAAAAAGACATAGGAGGTGGG	59.110	38.462	0.00	0.00	0.00	4.61
482	483	8.675504	TGAACACAAATAGGAAAACGAAACTAA	58.324	29.630	0.00	0.00	0.00	2.24
488	489	8.092068	TCTCTATGAACACAAATAGGAAAACGA	58.908	33.333	0.00	0.00	0.00	3.85
508	509	9.575783	GTCTTGTTCGAAAGTTCTTATCTCTAT	57.424	33.333	0.00	0.00	0.00	1.98
516	517	7.321745	AGATTTGTCTTGTTCGAAAGTTCTT	57.678	32.000	0.00	0.00	0.00	2.52
520	521	6.677781	TCAAGATTTGTCTTGTTCGAAAGT	57.322	33.333	15.43	0.00	45.26	2.66
575	576	9.846248	GACTATCAAATTGCAATACTTGAAACT	57.154	29.630	23.50	13.85	29.11	2.66
612	613	7.613801	GGGCAAAAGGATAATTAACCCAAAAAT	59.386	33.333	8.09	0.00	34.82	1.82
658	659	1.473677	TCGCATCTGAGGGCAAAATTG	59.526	47.619	5.18	0.00	0.00	2.32
660	661	1.838112	TTCGCATCTGAGGGCAAAAT	58.162	45.000	5.18	0.00	0.00	1.82
687	688	2.356741	GCATGGACTAGGGGCAAAACTA	60.357	50.000	0.00	0.00	0.00	2.24
740	741	1.292061	TCAAAACGTTGACCTGTCGG	58.708	50.000	0.00	0.00	38.88	4.79
796	797	4.263905	TGCAAGGGTCTGAATAGAATTGGT	60.264	41.667	0.00	0.00	34.01	3.67
814	815	3.952675	ACAAGCCACGCGTGCAAG	61.953	61.111	33.17	22.52	41.40	4.01
910	912	2.085262	CGTGCTCTCTGTCGCTGTG	61.085	63.158	0.00	0.00	0.00	3.66
913	915	4.427661	GCCGTGCTCTCTGTCGCT	62.428	66.667	0.00	0.00	0.00	4.93
917	919	4.363990	CACCGCCGTGCTCTCTGT	62.364	66.667	0.00	0.00	32.04	3.41
959	963	0.392193	CCACAGCTAGCTTCCCACTG	60.392	60.000	16.46	5.33	0.00	3.66
960	964	0.545309	TCCACAGCTAGCTTCCCACT	60.545	55.000	16.46	0.00	0.00	4.00
1040	1121	0.679505	TGTGTGAGAAACCCTCCGAG	59.320	55.000	0.00	0.00	41.25	4.63
1218	1300	5.550290	TGCAGTTCATTCATCACAGTCTTA	58.450	37.500	0.00	0.00	0.00	2.10
1225	1307	5.618056	TCTTCTTGCAGTTCATTCATCAC	57.382	39.130	0.00	0.00	0.00	3.06
1283	1365	4.435436	CTCGTGCTGCGGCCACTA	62.435	66.667	16.57	4.72	41.72	2.74
1328	1410	2.034053	GCTAGCTCTCTATCAGTGCGTT	59.966	50.000	7.70	0.00	44.91	4.84
1389	1471	4.508124	GGTATTGGTAGTGCTTGATCTTCG	59.492	45.833	0.00	0.00	0.00	3.79
1456	1538	8.811017	TCCATACATTTTCAACATTACAACCAT	58.189	29.630	0.00	0.00	0.00	3.55
1692	1783	1.681229	TTTGGCCCATAGAGGAACCT	58.319	50.000	0.00	0.00	41.22	3.50
1694	1785	3.631250	TGAATTTGGCCCATAGAGGAAC	58.369	45.455	0.00	0.00	41.22	3.62
1696	1787	3.122480	TCTGAATTTGGCCCATAGAGGA	58.878	45.455	0.00	0.00	41.22	3.71
1698	1789	2.883386	GCTCTGAATTTGGCCCATAGAG	59.117	50.000	0.00	6.25	34.74	2.43
1699	1790	2.746142	CGCTCTGAATTTGGCCCATAGA	60.746	50.000	0.00	0.00	0.00	1.98
1700	1791	1.605710	CGCTCTGAATTTGGCCCATAG	59.394	52.381	0.00	0.00	0.00	2.23
1701	1792	1.064758	ACGCTCTGAATTTGGCCCATA	60.065	47.619	0.00	0.00	0.00	2.74
1702	1793	0.323725	ACGCTCTGAATTTGGCCCAT	60.324	50.000	0.00	0.00	0.00	4.00
1747	1838	2.381911	CTAATTGGATGCAGTTGGCCT	58.618	47.619	3.32	0.00	43.89	5.19
1840	1933	6.695278	TCAATTAGCTTCCACAAAAAGTTTCG	59.305	34.615	0.00	0.00	0.00	3.46
1991	2091	5.049612	GTGTAAACCTTTACCAGAACTGAGC	60.050	44.000	3.19	0.00	41.72	4.26
1997	2097	4.166531	ACCAGGTGTAAACCTTTACCAGAA	59.833	41.667	0.17	0.00	41.72	3.02
2005	2105	0.553819	TGGCACCAGGTGTAAACCTT	59.446	50.000	21.26	0.00	38.22	3.50
2117	2218	1.831652	CTTGGTTCGAGTCCCCAGCT	61.832	60.000	6.32	0.00	0.00	4.24
2169	2270	3.576982	CCATCTATCCTAGCGGTTACCAA	59.423	47.826	1.13	0.00	0.00	3.67
2279	2380	1.970640	ACCCTCCAAAATTTCAGTGCC	59.029	47.619	0.00	0.00	0.00	5.01
2310	2411	2.287308	TGGCAGTGCAAACATACGTTTC	60.287	45.455	18.61	0.00	43.57	2.78
2352	2453	4.019950	GCCACTCTAACCCTAAACCAAGTA	60.020	45.833	0.00	0.00	0.00	2.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.